It says in the Gemara that R' Yitzchak said to R' Nachman in the name of R' Yochanan "Jacob our forefather didn't die".
R' Nachman asked back "Did the eulogizers eulogize him, and the embalmers embalm him, and the buriers bury him, all for nothing?" R' Yitzchak replied, "I'm doresh a pasuk, 'fear not my servant Jacob... your offspring...': it compares him to his offspring: just as they're alive, so is he".

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In order to understand this answer, he first quotes the relevant Gemara. The Gemara begins with a Mishna which (according to R' Meir) says that according to a verse both Yoreh [the early rains] and Malkosh [the late rains] fall during Nissan.

R' Nachman asked R' Yitzchak "How could the Mishna say that Yoreh [rains] falls in Nissan, it [normally] falls in Cheshvan?" R' Yitzchak answered in the name of R' Yochanan that in the time of Yoel (the prophet) both Yoreh and Malkosh rains fell in Nissan.

The Gemara continues with another discussion between R' Nachman and R' Yitzchak (over how could Shmuel age so early, as he passed away at fifty two).

R' Yitzchak said (again) in the name of R' Yochanan that he aged early as a result of his prayer.

The Gemara then proceeds to tell the story of how R' Yitzchak and R' Nachman were sitting together for a meal. R' Nachman asked R' Yitzchak to say a Dvar Torah (a word of Torah). R' Yitzchak answered in the name of R' Nachman that one isn't permitted to talk in the middle of a meal, as the food may go down the windpipe.

After the meal, R' Yitzchak said in the name of R' Yochanan "Jacob our Forefather didn't die" etc.

The sequence of the Gemara seems to be a series of statements from R' Yitzchak in the name of R' Yochanan of how Hashem acts in a miraculous manner with Jews (the first is that the early rains fell out of season and provided Jews with food, and the second is that Shmuel got old as a result of his prayer).

Therefore, R' Nachman asked R' Yitzchak to say words of Torah. He knew the law that one isn't allowed to speak during a meal. However, he thought that the law only applies to saying something secular. However, since Torah protects one from harm, one can rely on that and speak Torah during a meal.

Therefore, R' Yitzchak had to explain the ruling of R' Yochanan (that the food may enter the windpipe). Since there was a clear and present danger, one is no longer allowed to rely on a miracle to save him.

Here R' Yitzchak said a new concept. Even though Hashem acts in a miraculous manner with Jews (as mentioned in the previous stories), nonetheless, Torah and it's commandments must be kept in a natural manner.

However, this could be explained in two ways:

This rule (that Torah and Mitzvos must be done in a natural manner) is a result of nature. Since nature is also Hashem's creation, Hashem doesn't want it to be nullified without due cause.

Torah and Mitzvos must affect the natural world. Therefore, they must obey its rules.

The difference between the two ways is that according to the first, Torah and Mitzvos are under "nature" and are "subservient" to nature (and Torah and Mitzvos must be kept only when it's naturally possible). According to the second way, Torah and Mitzvos in and of themselves are above nature, but they (Torah and Mitzvos) have to be done within nature.

TL;DR section:

Therefore, one comes back to the question. When R' Yitzchak said "Jacob our Forefather didn't die" he meant that since he was of the opinion that the second way was the correct way (to understand the limitation of nature on Torah and Mitzvos), therefore, Yaakov (who represented Torah, and was the choisest of the forefathers) was above nature. Therefore, unlike all other things in the "natural" world, he didn't die.

However, R' Nachman was of the first opinion. Therefore, he asked "did they eulogizers eulogize him ... for naught"?

His question was not "how could they" but why would the Torah (which is Truth) write something that was done "for naught"? Since it was written in the Torah (that Yaakov was buried) and they were commanded to bury him, the Torah must be under "nature" (since the Torah required his burial, even though the Torah says that he is alive, shows that "nature" could affect Torah).

However, R' Yitzchak answered "I am expounding a verse...." This verse shows that the statement "Yaakov didn't die" wasn't referring to his physical life as was seen by the Egyptians. It was referring to his physical life as expounded in the Torah.

Therefore there is no contradiction (according to R' Yitzchak) how could the Torah command Yaakov to be buried, while at the same time saying that he is physically alive. Similar to Torah and Mitzvos, which (according to R' Yitzchak's understanding) are in essence above the world, yet their actions must be within nature (and nature "affects" truth), so too Yaakov's life, even though in essence he is physically alive, nonetheless, Torah (of truth) required his burial.

@Alex For Yaakov to be "literally alive", he would need a pulse. Otherwise, it's a new definition of "alive" and not a literal reading. So did he have a pulse or not? Or is this some sort of statement by the Torah about the braindeath debate? :P
–
aviJan 9 '12 at 14:39

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@ShmuelBrill Are you aware that is a new definition of the word "alive"?
–
aviJan 9 '12 at 18:03

The Torah Temima on Bereshit 49:33 goes through the gemara and explains. The gemara (Ta'anit 5b) goes through a list of instances where R Nachman would ask R Yitzchak a question and R Yitzchak would give an answer he heard from R Yochanan. In this specific part, R Nachman asked for a dvar torah from R Yitzchak while at a meal. R Yitchak answered that R Yochanan says "no talking during the meal" and later gives his d'var torah of Ya'akov avinu lo met. (I'm assuming from the question that you know the rest of the gemara.)

The Torah Temima points out that R Yitzchak's original answer is kinda strange (and rude too, seeing how R Nachman asked for a derasha while at a meal). We talk during meals every day and we rarely suffocate because of it! Rather, specifically in this case, R Yitzchak didn't want to give his derasha at a meal because he wanted to present it in a shocking manner, one which would result in an immediate outcry, and may result in a choking hazard due to the impulse to respond to a shocking statement as R Nachman did. After he made a strong impression with his shocking statement, he gave his pasuk, which most acharonim read allegorically (Maharsh"a and Torah Temima himself).

The statement wasn't actually literal, even though at first it was supposed to seem so, which is why no answer is necessary, yet the question was still valid when asked.

In the "Parshat HaShavua Chat", I gave Abarbanel's explanation of what R' Yochanan meant when he said that Yaakov did not die. The explanation is that Yaakov, in that the nation of Israel is called by his name still today, did not die, but lives on; i.e. his name lives on.

Abarbanel there also gives an explanation for the dialogue in the gemara (which he understands was between R' Yochanan and unnamed others). I will summarize:

R' Yochanan notices that the verse (Bereshis 49:33) says "וַיְכַל יַעֲקֹב לְצַוֹּת אֶת בָּנָיו וַיֶּאֱסֹף רַגְלָיו אֶל הַמִּטָּה וַיִּגְוַע וַיֵּאָסֶף אֶל עַמָּיו", but never says the words "וימת יעקב" like it does with the other avos when they died, and even Moshe when he died. R' Yochanan therefore said "Yaakov did not die", by which he is pointing out this omission in the pasuk, and which he understands as I mentioned above (his name lives on in that the nation is called by his name).

Now, R' Nachman (or Abarbanel's unnamed others) object: "But did the embalmers not embalm him, and did his children not bury him?" R' Nachman did not understand R' Yochanan's intentions and mistakenly took his words literally.

To this R' Yochanan (or R' Yitzchak) responds. But rather than explain his non-literalism, he instead explains the reasoning and source for the idea that was actually intended with his original statement. That is, this idea of Yaakov's name living on is not really sourced directly from the omision of the phrase in Bereshis 49:33, but rather "מקרא אני דורש" — I am deriving this idea directly from another verse [and from there applying the idea as a reason why the verse in Bereshis omitted the phrase specifying Yaakov's death]. The other verse is Yirmiyahu 30:10: (Mechon-Mamre translation)

Therefore fear thou not, O Jacob My servant, saith the LORD; neither be dismayed, O Israel; for, lo, I will save thee from afar, and thy seed from the land of their captivity; and Jacob shall again be quiet and at ease, and none shall make him afraid.

The unasked question here is that this verse seems to be speaking directly to Yaakov/ Yisrael as an individual ("הִנְנִי מוֹשִׁיעֲךָ" in the singular; "וְאֶת זַרְעֲךָ" - "your descendants") instead of to the nation as a people. Now, that this verse is addressed to Yaakov even though he is, of course, dead is not a problem. Yirmiyahu has poetic license. But how is he promising that Yaakov himself will be "saved", when we know that it is actually the nation of Israel that will be saved?

The answer is that Yaakov will be saved in that his name will continue to live in the sense mentioned above and not die out by his descendants being assimilated or annihilated. Thus, Yaakov/ Yisrael is saved in that his nation will be saved. He continues to "live" in that his nation continues to live. And this is what R' Yochanan (or R' Yitzchak) means by "מקיש הוא לזרעו מה זרעו בחיים אף הוא בחיים". So long as his nation lives and continues to be called by his name, he lives on.

This idea we learn from the above verse in Yirmiyahu, and that is why the verse in Bershis omits the phrase "וימת יעקב". This is what R' Yochanan is saying he meant when he said "יעקב אבינו לא מת".